2HLD

Crystal structure of yeast mitochondrial F1-ATPase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Novel features of the rotary catalytic mechanism revealed in the structure of yeast F(1) ATPase.

Kabaleeswaran, V.Puri, N.Walker, J.E.Leslie, A.G.Mueller, D.M.

(2006) Embo J. 25: 5433-5442

  • DOI: 10.1038/sj.emboj.7601410
  • Also Cited By: 3ZRY, 2WPD

  • PubMed Abstract: 
  • The crystal structure of yeast mitochondrial F(1) ATPase contains three independent copies of the complex, two of which have similar conformations while the third differs in the position of the central stalk relative to the alpha(3)beta(3) sub-assemb ...

    The crystal structure of yeast mitochondrial F(1) ATPase contains three independent copies of the complex, two of which have similar conformations while the third differs in the position of the central stalk relative to the alpha(3)beta(3) sub-assembly. All three copies display very similar asymmetric features to those observed for the bovine enzyme, but the yeast F(1) ATPase structures provide novel information. In particular, the active site that binds ADP in bovine F(1) ATPase has an ATP analog bound and therefore this structure does not represent the ADP-inhibited form. In addition, one of the complexes binds phosphate in the nucleotide-free catalytic site, and comparison with other structures provides a picture of the movement of the phosphate group during initial binding and subsequent catalysis. The shifts in position of the central stalk between two of the three copies of yeast F(1) ATPase and when these structures are compared to those of the bovine enzyme give new insight into the conformational changes that take place during rotational catalysis.


    Related Citations: 
    • Structure at 2.8 A resolution of F1-ATPase from bovine heart mitochondria
      Abrahams, J.P.,Leslie, A.G.,Lutter, R.,Walker, J.E.
      (1994) Nature 370: 594
    • The structure of the central stalk in bovine F1-ATPase at 2.4 A resolution
      Gibbons, C.,Montgomery, M.G.,Leslie, A.G.,Walker, J.E.
      (2000) Nat.Struct.Mol.Biol. 7: 1055
    • The structure of bovine F1-ATPase inhibited by ADP and beryllium fluoride.
      Kagawa, R.,Montgomery, M.G.,Braig, K.,Leslie, A.G.,Walker, J.E.
      (2004) Embo J. 23: 2734
    • Structure of bovine mitochondrial F(1)-ATPase with nucleotide bound to all three catalytic sites: implications for the mechanism of rotary catalysis.
      Menz, R.I.,Walker, J.E.,Leslie, A.G.
      (2001) Cell 106: 331
    • Molecular architecture of the rotary motor in ATP synthase.
      Stock, D.,Leslie, A.G.,Walker, J.E.
      (1999) Science 286: 1700
    • Crystallization and preliminary crystallographic studies of the mitochondrial F1-ATPase from the yeast Saccharomyces cerevisiae.
      Mueller, D.M.,Puri, N.,Kabaleeswaran, V.,Terry, C.,Leslie, A.G.,Walker, J.E.
      (2004) Acta Crystallogr.,Sect.D 60: 1441


    Organizational Affiliation

    Department of Biochemistry & Molecular Biology, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP synthase alpha chain, mitochondrial
A, B, C, J, K, L, S, T, U
510Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ATP1
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
ATP synthase (F1c10)
Find proteins for P07251 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07251
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP synthase beta chain, mitochondrial
D, E, F, M, N, O, V, W, X
478Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ATP2
EC: 3.6.3.14
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
ATP synthase (F1c10)
Find proteins for P00830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00830
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ATP synthase gamma chain, mitochondrial
G, P, Y
278Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ATP3 (ATP3a, ATP3b)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
ATP synthase (F1c10)
Find proteins for P38077 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38077
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ATP synthase delta chain, mitochondrial
H, Q, Z
138Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ATP16
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
ATP synthase (F1c10)
Find proteins for Q12165 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12165
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
ATP synthase epsilon chain, mitochondrial
I, R, 1
61Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ATP15
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
ATP synthase (F1c10)
Find proteins for P21306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P21306
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
N
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ANP
Query on ANP

Download SDF File 
Download CCD File 
A, B, C, D, F, J, K, L, M, O, S, T, U, V, X
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, F, J, K, L, M, O, S, T, U, V, X
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 111.524α = 90.00
b = 294.132β = 101.67
c = 190.432γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CCP4data scaling
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-28
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance